Job ID = 6455014 SRX = SRX2638361 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:47:10 prefetch.2.10.7: 1) Downloading 'SRR5341686'... 2020-06-21T09:47:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:51:08 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:51:09 prefetch.2.10.7: 1) 'SRR5341686' was downloaded successfully Read 28970111 spots for SRR5341686/SRR5341686.sra Written 28970111 spots for SRR5341686/SRR5341686.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:24 28970111 reads; of these: 28970111 (100.00%) were unpaired; of these: 22265502 (76.86%) aligned 0 times 2665748 (9.20%) aligned exactly 1 time 4038861 (13.94%) aligned >1 times 23.14% overall alignment rate Time searching: 00:05:24 Overall time: 00:05:24 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_rmdupse_core] 5655672 / 6704609 = 0.8435 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 18:59:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2638361/SRX2638361.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2638361/SRX2638361.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2638361/SRX2638361.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2638361/SRX2638361.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 21 Jun 2020 18:59:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:59:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:59:43: 1000000 INFO @ Sun, 21 Jun 2020 18:59:43: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:59:43: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:59:43: #1 total tags in treatment: 1048937 INFO @ Sun, 21 Jun 2020 18:59:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:59:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:59:43: #1 tags after filtering in treatment: 1048641 INFO @ Sun, 21 Jun 2020 18:59:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:59:43: #1 finished! INFO @ Sun, 21 Jun 2020 18:59:43: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:59:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:59:43: #2 number of paired peaks: 3310 INFO @ Sun, 21 Jun 2020 18:59:43: start model_add_line... INFO @ Sun, 21 Jun 2020 18:59:43: start X-correlation... INFO @ Sun, 21 Jun 2020 18:59:43: end of X-cor INFO @ Sun, 21 Jun 2020 18:59:43: #2 finished! INFO @ Sun, 21 Jun 2020 18:59:43: #2 predicted fragment length is 164 bps INFO @ Sun, 21 Jun 2020 18:59:43: #2 alternative fragment length(s) may be 164 bps INFO @ Sun, 21 Jun 2020 18:59:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2638361/SRX2638361.05_model.r INFO @ Sun, 21 Jun 2020 18:59:43: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:59:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:59:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:59:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2638361/SRX2638361.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:59:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2638361/SRX2638361.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:59:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2638361/SRX2638361.05_summits.bed INFO @ Sun, 21 Jun 2020 18:59:48: Done! pass1 - making usageList (525 chroms): 1 millis pass2 - checking and writing primary data (2184 records, 4 fields): 16 millis CompletedMACS2peakCalling WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 19:00:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2638361/SRX2638361.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2638361/SRX2638361.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2638361/SRX2638361.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2638361/SRX2638361.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 21 Jun 2020 19:00:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:00:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:00:13: 1000000 INFO @ Sun, 21 Jun 2020 19:00:13: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:00:13: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:00:13: #1 total tags in treatment: 1048937 INFO @ Sun, 21 Jun 2020 19:00:13: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:00:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:00:13: #1 tags after filtering in treatment: 1048641 INFO @ Sun, 21 Jun 2020 19:00:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:00:13: #1 finished! INFO @ Sun, 21 Jun 2020 19:00:13: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:00:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:00:13: #2 number of paired peaks: 3310 INFO @ Sun, 21 Jun 2020 19:00:13: start model_add_line... INFO @ Sun, 21 Jun 2020 19:00:13: start X-correlation... INFO @ Sun, 21 Jun 2020 19:00:13: end of X-cor INFO @ Sun, 21 Jun 2020 19:00:13: #2 finished! INFO @ Sun, 21 Jun 2020 19:00:13: #2 predicted fragment length is 164 bps INFO @ Sun, 21 Jun 2020 19:00:13: #2 alternative fragment length(s) may be 164 bps INFO @ Sun, 21 Jun 2020 19:00:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2638361/SRX2638361.10_model.r INFO @ Sun, 21 Jun 2020 19:00:13: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:00:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:00:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:00:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2638361/SRX2638361.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:00:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2638361/SRX2638361.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:00:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2638361/SRX2638361.10_summits.bed INFO @ Sun, 21 Jun 2020 19:00:18: Done! pass1 - making usageList (281 chroms): 1 millis pass2 - checking and writing primary data (896 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 19:00:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2638361/SRX2638361.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2638361/SRX2638361.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2638361/SRX2638361.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2638361/SRX2638361.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 21 Jun 2020 19:00:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:00:36: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:00:43: 1000000 INFO @ Sun, 21 Jun 2020 19:00:43: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:00:43: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:00:43: #1 total tags in treatment: 1048937 INFO @ Sun, 21 Jun 2020 19:00:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:00:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:00:43: #1 tags after filtering in treatment: 1048641 INFO @ Sun, 21 Jun 2020 19:00:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:00:43: #1 finished! INFO @ Sun, 21 Jun 2020 19:00:43: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:00:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:00:44: #2 number of paired peaks: 3310 INFO @ Sun, 21 Jun 2020 19:00:44: start model_add_line... INFO @ Sun, 21 Jun 2020 19:00:44: start X-correlation... INFO @ Sun, 21 Jun 2020 19:00:44: end of X-cor INFO @ Sun, 21 Jun 2020 19:00:44: #2 finished! INFO @ Sun, 21 Jun 2020 19:00:44: #2 predicted fragment length is 164 bps INFO @ Sun, 21 Jun 2020 19:00:44: #2 alternative fragment length(s) may be 164 bps INFO @ Sun, 21 Jun 2020 19:00:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2638361/SRX2638361.20_model.r INFO @ Sun, 21 Jun 2020 19:00:44: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:00:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:00:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:00:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2638361/SRX2638361.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:00:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2638361/SRX2638361.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:00:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2638361/SRX2638361.20_summits.bed INFO @ Sun, 21 Jun 2020 19:00:48: Done! pass1 - making usageList (106 chroms): 1 millis pass2 - checking and writing primary data (349 records, 4 fields): 4 millis CompletedMACS2peakCalling